Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002053.1 Kokia drynarioides strain JFW-HI SEQ_113945, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 58273
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:665 original size:41 final size:41
Alignment explanation
Indices: 582--1003 Score: 345
Period size: 41 Copynumber: 10.4 Consensus size: 41
572 AATGTATCAA
* * * *** * *
582 TATTGCTATGACTTTTAGCGACGCTTTTTCATAAGTGTCGC
1 TATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAGAGCCGC
* *
623 TATTGCTCTGATCTTTAGCGGCGCTTGCCCTTAAGAGCCGC
1 TATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAGAGCCGC
* * * *
664 TATTGTTATGATCTTTAGCGGTGCTTGCCCATAAGCA-CCGC
1 TATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAG-AGCCGC
* * * * * *
705 TATTGCTCTGACCTTTAGCGACACTT-TCCATAAGCGTCAC
1 TATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAGAGCCGC
* * ** * * *
745 TATTGCACTGACCTTTAGTGGCGCTTTTCAAGAAGTGCCGC
1 TATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAGAGCCGC
* * * * *
786 TATTGCTCTAACCTTTTGCGGCGCTT-TCCATAAGCGCTGC
1 TATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAGAGCCGC
* * *
826 TACTACTCTGACCTTTAGCGGCGCTTGCCCATAA-ACGCCTC
1 TATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAGA-GCCGC
** * * * *
867 TATTGCTCTGACCTTTAGCGGCGCTTTACAAAAAGCGCAGC
1 TATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAGAGCCGC
* *
908 TATTGC-CTGATCTTTAGCGGCGCTTACCCATAAGCA-CCGC
1 TATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAG-AGCCGC
* * * *
948 TATTGCTCTAACCTTTAGCGGCGCTTTCCCATAAGTGTCGC
1 TATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAGAGCCGC
989 TATTGCTCT-ACCTTT
1 TATTGCTCTGACCTTT
1004 TACGGCGTTT
Statistics
Matches: 302, Mismatches: 70, Indels: 19
0.77 0.18 0.05
Matches are distributed among these distances:
40 101 0.33
41 200 0.66
42 1 0.00
ACGTcount: A:0.19, C:0.28, G:0.20, T:0.33
Consensus pattern (41 bp):
TATTGCTCTGACCTTTAGCGGCGCTTGCCCATAAGAGCCGC
Found at i:858 original size:122 final size:121
Alignment explanation
Indices: 582--1003 Score: 391
Period size: 122 Copynumber: 3.5 Consensus size: 121
572 AATGTATCAA
* * * ** * * *
582 TATTGCTATGACTTTTAGCGACGCTTTTTCATAAGTGTCGCTATTGCTCTGATCTTTAGCGGCGC
1 TATTGCTCTGACCTTTAGCGGCGC-TTCCCATAAGCGTCACTATTGCTCTGACCTTTAGCGGCGC
** *** * * * * * *
647 TTGCCCTTAAGAGCCGCTATTG-TTATGATCTTTAGCGGTGCTTGCCCATAAGCACCGC
65 TTTACAAAAAGCGCAGCTATTGCCTA--ACCTTTAGCGGCGCTTACCCATAAGCACCGC
* * * * *
705 TATTGCTCTGACCTTTAGCGACACTTTCCATAAGCGTCACTATTGCACTGACCTTTAGTGGCGCT
1 TATTGCTCTGACCTTTAGCGGCGCTTCCCATAAGCGTCACTATTGCTCTGACCTTTAGCGGCGCT
* * * * * * * *
770 TTTCAAGAAGTGCCGCTATTGCTCTAACCTTTTGCGGCGCTT-TCCATAAGCGCTGC
66 TTACAAAAAGCGCAGCTATTGC-CTAACCTTTAGCGGCGCTTACCCATAAGCACCGC
* * * * *
826 TACTACTCTGACCTTTAGCGGCGCTTGCCCATAAACGCCTCTATTGCTCTGACCTTTAGCGGCGC
1 TATTGCTCTGACCTTTAGCGGCGCTT-CCCATAAGCGTCACTATTGCTCTGACCTTTAGCGGCGC
* *
891 TTTACAAAAAGCGCAGCTATTGCCTGATCTTTAGCGGCGCTTACCCATAAGCACCGC
65 TTTACAAAAAGCGCAGCTATTGCCTAACCTTTAGCGGCGCTTACCCATAAGCACCGC
* * *
948 TATTGCTCTAACCTTTAGCGGCGCTTTCCCATAAGTGTCGCTATTGCTCT-ACCTTT
1 TATTGCTCTGACCTTTAGCGGCGC-TTCCCATAAGCGTCACTATTGCTCTGACCTTT
1004 TACGGCGTTT
Statistics
Matches: 245, Mismatches: 49, Indels: 12
0.80 0.16 0.04
Matches are distributed among these distances:
121 55 0.22
122 165 0.67
123 23 0.09
124 2 0.01
ACGTcount: A:0.19, C:0.28, G:0.20, T:0.33
Consensus pattern (121 bp):
TATTGCTCTGACCTTTAGCGGCGCTTCCCATAAGCGTCACTATTGCTCTGACCTTTAGCGGCGCT
TTACAAAAAGCGCAGCTATTGCCTAACCTTTAGCGGCGCTTACCCATAAGCACCGC
Found at i:872 original size:162 final size:163
Alignment explanation
Indices: 620--982 Score: 435
Period size: 162 Copynumber: 2.2 Consensus size: 163
610 TCATAAGTGT
* * * * * * * ** * *
620 CGCTATTGCTCTGATCTTTAGCGGCGCTTGCCCTTAAGAGCCGCTATTGTTATGATCTTTAGCGG
1 CGCTATTGCTCTAACCTTTAGCGGCGCTTTCCCATAAGCGCTGCTACTACTCTGACCTTTAGCGG
* * * *
685 TGCTTGCCCATAAGCACCGCTATTGCTCTGACCTTTAGCGACACTTT-CCATAAGCGTCA-CTAT
66 CGCTTGCCCATAAACACCGCTATTGCTCTGACCTTTAGCGACACTTTACAAAAAGCG-CAGCTAT
* ** **
748 TGCACTGACCTTTAGTGGCGCTTTTCAAGAAGTGC
130 TGC-CTGACCTTTAGCGGCGCTTACCAAGAAGCAC
*
783 CGCTATTGCTCTAACCTTTTGCGGCGCTTT-CCATAAGCGCTGCTACTACTCTGACCTTTAGCGG
1 CGCTATTGCTCTAACCTTTAGCGGCGCTTTCCCATAAGCGCTGCTACTACTCTGACCTTTAGCGG
* * * *
847 CGCTTGCCCATAAACGCCTCTATTGCTCTGACCTTTAGCGGCGCTTTACAAAAAGCGCAGCTATT
66 CGCTTGCCCATAAACACCGCTATTGCTCTGACCTTTAGCGACACTTTACAAAAAGCGCAGCTATT
* * *
912 GCCTGATCTTTAGCGGCGCTTACCCATAAGCAC
131 GCCTGACCTTTAGCGGCGCTTACCAAGAAGCAC
945 CGCTATTGCTCTAACCTTTAGCGGCGCTTTCCCATAAG
1 CGCTATTGCTCTAACCTTTAGCGGCGCTTTCCCATAAG
983 TGTCGCTATT
Statistics
Matches: 168, Mismatches: 29, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
162 121 0.72
163 47 0.28
ACGTcount: A:0.19, C:0.29, G:0.20, T:0.31
Consensus pattern (163 bp):
CGCTATTGCTCTAACCTTTAGCGGCGCTTTCCCATAAGCGCTGCTACTACTCTGACCTTTAGCGG
CGCTTGCCCATAAACACCGCTATTGCTCTGACCTTTAGCGACACTTTACAAAAAGCGCAGCTATT
GCCTGACCTTTAGCGGCGCTTACCAAGAAGCAC
Found at i:1010 original size:81 final size:80
Alignment explanation
Indices: 620--1003 Score: 394
Period size: 81 Copynumber: 4.7 Consensus size: 80
610 TCATAAGTGT
* * * * * * *
620 CGCTATTGCTCTGATCTTTAGCGGCGCTTGCCCTTAAGAGCCGCTATTGTTATGATCTTTAGCGG
1 CGCTATTGCTCTGACCTTTAGCGGCGCTT-TCCATAAGCG-CGCTATTGCTCTGACCTTTAGCGG
*
685 TGCTTGCCCATAAGCAC
64 CGCTTGCCCATAAGCAC
* * * * *
702 CGCTATTGCTCTGACCTTTAGCGACACTTTCCATAAGCGTCACTATTGCACTGACCTTTAGTGGC
1 CGCTATTGCTCTGACCTTTAGCGGCGCTTTCCATAAGCG-CGCTATTGCTCTGACCTTTAGCGGC
** * * **
767 GCTTTTCAAGAAGTGC
65 GCTTGCCCATAAGCAC
* * * *
783 CGCTATTGCTCTAACCTTTTGCGGCGCTTTCCATAAGCGCTGCTACTACTCTGACCTTTAGCGGC
1 CGCTATTGCTCTGACCTTTAGCGGCGCTTTCCATAAGCGC-GCTATTGCTCTGACCTTTAGCGGC
* *
848 GCTTGCCCATAAACGC
65 GCTTGCCCATAAGCAC
* * * *
864 CTCTATTGCTCTGACCTTTAGCGGCGCTTTACAAAAAGCGCAGCTATTGC-CTGATCTTTAGCGG
1 CGCTATTGCTCTGACCTTTAGCGGCGCTTT-CCATAAGCGC-GCTATTGCTCTGACCTTTAGCGG
*
928 CGCTTACCCATAAGCAC
64 CGCTTGCCCATAAGCAC
* *
945 CGCTATTGCTCTAACCTTTAGCGGCGCTTTCCCATAAGTGTCGCTATTGCTCT-ACCTTT
1 CGCTATTGCTCTGACCTTTAGCGGCGCTTT-CCATAAGCG-CGCTATTGCTCTGACCTTT
1004 TACGGCGTTT
Statistics
Matches: 244, Mismatches: 54, Indels: 9
0.79 0.18 0.03
Matches are distributed among these distances:
80 1 0.00
81 200 0.82
82 43 0.18
ACGTcount: A:0.19, C:0.29, G:0.20, T:0.32
Consensus pattern (80 bp):
CGCTATTGCTCTGACCTTTAGCGGCGCTTTCCATAAGCGCGCTATTGCTCTGACCTTTAGCGGCG
CTTGCCCATAAGCAC
Found at i:7707 original size:26 final size:26
Alignment explanation
Indices: 7658--7709 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
7648 TTTAGTTATT
* *
7658 ATTATTTGATATTTGATAGTTTTACA
1 ATTATTTGATATTTAATAATTTTACA
7684 ATTATTTGAT-TTTAATAATATTTACA
1 ATTATTTGATATTTAATAAT-TTTACA
7710 TAGTTGTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.54
Consensus pattern (26 bp):
ATTATTTGATATTTAATAATTTTACA
Found at i:9915 original size:27 final size:27
Alignment explanation
Indices: 9885--9995 Score: 168
Period size: 27 Copynumber: 4.1 Consensus size: 27
9875 CTGAGCAATA
9885 AGCGATATTCTGTATCTGGCTCGAATG
1 AGCGATATTCTGTATCTGGCTCGAATG
*
9912 AGCGATATTCTGTATCTGGCTCGTATG
1 AGCGATATTCTGTATCTGGCTCGAATG
* * *
9939 AGAGACATTCTGTATCTGCCTCGAATG
1 AGCGATATTCTGTATCTGGCTCGAATG
* *
9966 AGCGATATTTTGTATTTGGCTCGAATG
1 AGCGATATTCTGTATCTGGCTCGAATG
9993 AGC
1 AGC
9996 TGTATCTGGC
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 74 1.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (27 bp):
AGCGATATTCTGTATCTGGCTCGAATG
Found at i:10005 original size:20 final size:20
Alignment explanation
Indices: 9976--10020 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
9966 AGCGATATTT
* **
9976 TGTATTTGGCTCGAATGAGC
1 TGTATCTGGCTCGAAAAAGC
9996 TGTATCTGGCTCGAAAAAGC
1 TGTATCTGGCTCGAAAAAGC
10016 TGTAT
1 TGTAT
10021 TTTTCTATTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (20 bp):
TGTATCTGGCTCGAAAAAGC
Found at i:11134 original size:22 final size:22
Alignment explanation
Indices: 11109--11152 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
11099 ATACAATTTC
*
11109 AAATTATATCTGA-ATTTAAATA
1 AAATTAAATC-GATATTTAAATA
11131 AAATTAAATCGATATTTAAATA
1 AAATTAAATCGATATTTAAATA
11153 CTTTATGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 2 0.10
22 18 0.90
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.39
Consensus pattern (22 bp):
AAATTAAATCGATATTTAAATA
Found at i:11541 original size:69 final size:69
Alignment explanation
Indices: 11428--11566 Score: 269
Period size: 69 Copynumber: 2.0 Consensus size: 69
11418 CTATGCCCAC
*
11428 AAAAGACCCATTGCATGACACAGCTCCATCTGTATTGAGTTTGACCCATCTTCTGTTCAACCTTG
1 AAAAGACCCATTGCATGACACAGCTCCATCTGTATTGAGCTTGACCCATCTTCTGTTCAACCTTG
11493 ACCA
66 ACCA
11497 AAAAGACCCATTGCATGACACAGCTCCATCTGTATTGAGCTTGACCCATCTTCTGTTCAACCTTG
1 AAAAGACCCATTGCATGACACAGCTCCATCTGTATTGAGCTTGACCCATCTTCTGTTCAACCTTG
11562 ACCA
66 ACCA
11566 A
1 A
11567 TGTGTGGTAG
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.28
Consensus pattern (69 bp):
AAAAGACCCATTGCATGACACAGCTCCATCTGTATTGAGCTTGACCCATCTTCTGTTCAACCTTG
ACCA
Found at i:12134 original size:21 final size:23
Alignment explanation
Indices: 12087--12135 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 23
12077 ACTAATTCTC
*
12087 ATTT-AATTAGTAAATATATTTT
1 ATTTAAATTAGTAAATATATATT
*
12109 CTTTAAATTA-TAAA-ATATATT
1 ATTTAAATTAGTAAATATATATT
12130 ATTTAA
1 ATTTAA
12136 TAATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 11 0.48
22 7 0.30
23 5 0.22
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATTTAAATTAGTAAATATATATT
Found at i:12771 original size:23 final size:26
Alignment explanation
Indices: 12722--12771 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 26
12712 CATATATACT
*
12722 TTTACCTAAAATAATATATATAATTA
1 TTTACCTAAAATAATATAAATAATTA
12748 TTTACC-AAAA-AA-ATAAATAATTA
1 TTTACCTAAAATAATATAAATAATTA
12771 T
1 T
12772 ATAAAGGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 2 0.09
25 4 0.17
26 6 0.26
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (26 bp):
TTTACCTAAAATAATATAAATAATTA
Found at i:25900 original size:24 final size:24
Alignment explanation
Indices: 25868--25918 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
25858 AGAAATAATC
*
25868 TTTCAATTAAATTATGTTTAATTA
1 TTTCAATTAAACTATGTTTAATTA
* *
25892 TTTCAATTAAACTCTGTTTATTTA
1 TTTCAATTAAACTATGTTTAATTA
25916 TTT
1 TTT
25919 GAGTCAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.31, C:0.08, G:0.04, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTATGTTTAATTA
Found at i:26091 original size:9 final size:8
Alignment explanation
Indices: 26063--26087 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
26053 AGGGTTTTTT
26063 GTTTTCGG
1 GTTTTCGG
26071 GTTTTCGG
1 GTTTTCGG
26079 GTTTTCGG
1 GTTTTCGG
26087 G
1 G
26088 GTTTAGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.40, T:0.48
Consensus pattern (8 bp):
GTTTTCGG
Found at i:29277 original size:3 final size:3
Alignment explanation
Indices: 29269--29299 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
29259 TATGAAACCA
29269 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
29300 CCTTTCTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:36807 original size:20 final size:20
Alignment explanation
Indices: 36764--36807 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
36754 AAATCATTAA
* *
36764 TTAAAAATAAAAAAATATTT
1 TTAAAAATAAAAAAATAGTG
36784 TTAAAAATAAAACAAAT-GTG
1 TTAAAAATAAAA-AAATAGTG
36804 TTAA
1 TTAA
36808 TATCTAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (20 bp):
TTAAAAATAAAAAAATAGTG
Found at i:37142 original size:13 final size:13
Alignment explanation
Indices: 37113--37178 Score: 80
Period size: 13 Copynumber: 5.1 Consensus size: 13
37103 CTTAAACCAA
37113 ACTTTTCAAAA-C
1 ACTTTTCAAAAGC
*
37125 TACTTCTCAAAAGC
1 -ACTTTTCAAAAGC
* *
37139 ACTTTTCTAGAGC
1 ACTTTTCAAAAGC
*
37152 ACTTTTTAAAAGC
1 ACTTTTCAAAAGC
37165 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
37178 A
1 A
37179 ATGCTAAACT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
13 43 0.98
14 1 0.02
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.33
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:39615 original size:6 final size:6
Alignment explanation
Indices: 39604--39641 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
39594 GGCAGCCTCT
* *
39604 AAATCG AAATCG AAATCG AAAACG AAAACG AAAT-G AAA
1 AAATCG AAATCG AAATCG AAATCG AAATCG AAATCG AAA
39642 ATCAAAAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 4 0.13
6 26 0.87
ACGTcount: A:0.61, C:0.13, G:0.16, T:0.11
Consensus pattern (6 bp):
AAATCG
Found at i:39843 original size:5 final size:5
Alignment explanation
Indices: 39833--39860 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
39823 GTGAGGGAAA
39833 GGGGT GGGGT GGGGT GGGGT GGGGT GGG
1 GGGGT GGGGT GGGGT GGGGT GGGGT GGG
39861 AAGAAAAGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.82, T:0.18
Consensus pattern (5 bp):
GGGGT
Found at i:40280 original size:22 final size:23
Alignment explanation
Indices: 40241--40284 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
40231 GACAATTGGA
*
40241 ATATATTTAATATCTTTAATTTG
1 ATATATTTAATATATTTAATTTG
*
40264 ATATA-TTAATTTATTTAATTT
1 ATATATTTAATATATTTAATTT
40285 TTTTTTTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (23 bp):
ATATATTTAATATATTTAATTTG
Found at i:45025 original size:38 final size:40
Alignment explanation
Indices: 44939--45031 Score: 120
Period size: 38 Copynumber: 2.4 Consensus size: 40
44929 CTAAACTGGT
* *
44939 AGTGACACTGTAAACACTGCAATATTACAATTGAATTGGC
1 AGTGACACTGTAAACACTGCAATACTACAACTGAATTGGC
44979 AGTGACACTGTAAACACT-CAATACTAC-ACTGAA-TGGAC
1 AGTGACACTGTAAACACTGCAATACTACAACTGAATTGG-C
* *
45017 TGTTACACTGTAAAC
1 AGTGACACTGTAAAC
45032 CCCGCCATGC
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
37 3 0.06
38 19 0.40
39 8 0.17
40 18 0.38
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (40 bp):
AGTGACACTGTAAACACTGCAATACTACAACTGAATTGGC
Found at i:52402 original size:20 final size:20
Alignment explanation
Indices: 52373--52416 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
52363 TTTGCAATTC
52373 AAATATTTATA-GTAA-TTTT
1 AAATATTTATATG-AATTTTT
52392 AAATAATTTATATGAATTTTT
1 AAAT-ATTTATATGAATTTTT
52413 AAAT
1 AAAT
52417 TTAATAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.18
20 9 0.41
21 9 0.41
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (20 bp):
AAATATTTATATGAATTTTT
Found at i:52428 original size:17 final size:18
Alignment explanation
Indices: 52396--52429 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
52386 AATTTTAAAT
*
52396 AATTTATATGAATTTTTA
1 AATTTATATAAATTTTTA
52414 AATTTA-ATAAATTTTT
1 AATTTATATAAATTTTT
52430 GAATAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (18 bp):
AATTTATATAAATTTTTA
Found at i:52443 original size:20 final size:19
Alignment explanation
Indices: 52388--52452 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 19
52378 TTTATAGTAA
*
52388 TTTTAAATAATTTATATGAAT
1 TTTTGAATAATTT-TAT-AAT
*
52409 TTTT--A-AATTTAATAAAT
1 TTTTGAATAATTTTAT-AAT
52426 TTTTGAATAATTTTATAAT
1 TTTTGAATAATTTTATAAT
52445 TATTTGAA
1 T-TTTGAA
52453 AATAAACATC
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
17 9 0.24
18 5 0.14
19 6 0.16
20 13 0.35
21 4 0.11
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
TTTTGAATAATTTTATAAT
Found at i:54193 original size:17 final size:17
Alignment explanation
Indices: 54167--54204 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
54157 AAATTTTATG
*
54167 AAAAATTTAAAGAT-TA
1 AAAAATTTAAACATATA
54183 AAAAATATTAAACATATA
1 AAAAAT-TTAAACATATA
54201 AAAA
1 AAAA
54205 CAAAAATTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 7 0.37
18 6 0.32
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (17 bp):
AAAAATTTAAACATATA
Found at i:55746 original size:14 final size:14
Alignment explanation
Indices: 55727--55777 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
55717 TTATTTGATA
55727 AACACATAATAAAT
1 AACACATAATAAAT
*
55741 AACACACTAAAAAAAT
1 AACACA-T-AATAAAT
**
55757 AACATTTAATAAAT
1 AACACATAATAAAT
55771 AACACAT
1 AACACAT
55778 GAAATGCGTA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
14 17 0.59
15 2 0.07
16 10 0.34
ACGTcount: A:0.63, C:0.16, G:0.00, T:0.22
Consensus pattern (14 bp):
AACACATAATAAAT
Found at i:58244 original size:2 final size:2
Alignment explanation
Indices: 58237--58268 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
58227 GAAGATTTGG
58237 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
58269 TTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.